Daniel:Notebook/GenomeMiner/2013-9-23: Difference between revisions

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>Djacobse
(Created page with "=Mock HL155 (Started 9/9/2013)= Back to Calendar ==Full Reference Sequence Reads== From [[Daniel:No...")
 
>Djacobse
 
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===Alignment Results===
===Alignment Results===


2959000 reads; of these:
2959000 reads; of these:
   2959000 (100.00%) were unpaired; of these:
   2959000 (100.00%) were unpaired; of these:
     105936 (3.58%) aligned 0 times
     105936 (3.58%) aligned 0 times
     2842493 (96.06%) aligned exactly 1 time
     2842493 (96.06%) aligned exactly 1 time
     10571 (0.36%) aligned >1 times
     10571 (0.36%) aligned >1 times
96.42% overall alignment rate
96.42% overall alignment rate


===Error Counting Results===
===Error Counting Results===

Latest revision as of 22:24, 24 September 2013

Mock HL155 (Started 9/9/2013)[edit]

Back to Calendar

Full Reference Sequence Reads[edit]

From Friday, I'm still trying to generate reads that use the entire reference sequence to generate the mock reads (important when deletions are present). Also, the current code does not allow 2 errors per base (but allows up to n errors per read where n is the number of bases in the read).

Workflow[edit]

1. MockHL155_Master.m, Switch 7
2. scp v4s1mockseq_extdel_errormimic.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/extdeletions/
3. hl155bash.sh
4. perl imp_count_mismatch.plx

MATLAB Error Counts[edit]

1494539 substitutions (1.01 pct reads) 
385509 insertions (0.26 pct reads) 
74012 deletions (0.05 pct reads) 

Alignment Results[edit]

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   105936 (3.58%) aligned 0 times
   2842493 (96.06%) aligned exactly 1 time
   10571 (0.36%) aligned >1 times
96.42% overall alignment rate

Error Counting Results[edit]

Error Rate: 1.128%
Error Rate of Insertions: 0.189%
Error Rate of Deletions: 0.029%
Error Rate of Substitutions: 0.91%